Variant report

Variant	rs334559
Chromosome Location	chr3:119809605-119809606
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:119809493-119809715	Hela-S3	cervix:	n/a	n/a
2	CTCF	chr3:119809460-119809610	AG10803	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:119755863..119757873-chr3:119808761..119811166,2	K562	blood:
2	chr3:119707707..119709811-chr3:119807417..119810335,2	MCF-7	breast:
3	chr3:119594389..119596043-chr3:119808975..119811664,2	K562	blood:

Variant related genes	Relation type
ENSG00000242622	TF binding region
ENSG00000082701	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10433404	0.82[YRI][hapmap]
rs10934502	0.82[YRI][hapmap]
rs10934503	0.81[YRI][hapmap]
rs10934505	0.82[YRI][hapmap]
rs10934506	0.82[YRI][hapmap]
rs10934507	0.87[YRI][hapmap]
rs1154596	1.00[CHB][hapmap]
rs1154597	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11915717	0.82[YRI][hapmap]
rs11921053	0.91[EUR][1000 genomes]
rs12629015	0.82[YRI][hapmap]
rs12634476	0.82[YRI][hapmap]
rs12638973	0.81[YRI][hapmap]
rs13312998	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs13314595	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1574154	0.82[YRI][hapmap]
rs1579031	1.00[CEU][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16830683	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs16830689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs182839	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs184576	0.82[ASN][1000 genomes]
rs1870931	0.82[YRI][hapmap]
rs28516957	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs334533	0.82[CEU][hapmap]
rs334534	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs334535	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs334538	0.84[CHD][hapmap]
rs334552	0.84[ASN][1000 genomes]
rs334554	0.84[ASN][1000 genomes]
rs334560	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs334561	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs334566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4072520	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4340737	0.82[YRI][hapmap]
rs4688046	0.82[YRI][hapmap]
rs4688047	0.82[YRI][hapmap]
rs4688054	0.82[YRI][hapmap]
rs56126162	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58043853	0.91[EUR][1000 genomes]
rs6438554	1.00[CHB][hapmap]
rs6438555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66650215	0.82[EUR][1000 genomes]
rs6769435	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6770314	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6771023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs6774693	0.98[EUR][1000 genomes]
rs6775397	0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6779828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784239	1.00[CHB][hapmap]
rs6785050	1.00[CHB][hapmap]
rs6795874	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6797689	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs6802301	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805931	0.84[ASN][1000 genomes]
rs6807868	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7613197	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7617372	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.88[TSI][hapmap];0.82[ASN][1000 genomes]
rs7620750	1.00[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7628426	0.84[ASN][1000 genomes]
rs7636600	0.93[EUR][1000 genomes]
rs7644234	0.82[CEU][hapmap]
rs7649661	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7650554	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs7652172	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289138	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs968824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9851174	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9859778	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9879992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv3964	chr3:119786623-119831698	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
5	nsv829697	chr3:119802856-119918435	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119764600-119812000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:119799000-119810400	Weak transcription	Placenta	Placenta
3	chr3:119799200-119810600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:119804600-119812000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:119804600-119812000	Weak transcription	Pancreas	Pancrea
6	chr3:119805600-119810600	Weak transcription	Stomach Mucosa	stomach
7	chr3:119805600-119812000	Weak transcription	Gastric	stomach
8	chr3:119805800-119811400	Weak transcription	Esophagus	oesophagus
9	chr3:119807600-119809800	Enhancers	Liver	Liver
10	chr3:119807800-119810000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:119808000-119814800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:119808000-119816400	Active TSS	Fetal Brain Female	brain
13	chr3:119808200-119809800	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr3:119808200-119810600	Weak transcription	Small Intestine	intestine
15	chr3:119808200-119814800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:119808200-119815000	Active TSS	HMEC	breast
17	chr3:119808400-119812800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:119808400-119815600	Active TSS	GM12878-XiMat	blood
19	chr3:119808600-119810400	Flanking Active TSS	Dnd41	blood
20	chr3:119808600-119814800	Active TSS	NHEK	skin
21	chr3:119808800-119815000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:119808800-119815600	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr3:119809000-119810000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr3:119809000-119810400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr3:119809000-119810400	Flanking Active TSS	HUVEC	blood vessel
26	chr3:119809000-119811800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:119809000-119812800	Active TSS	Right Atrium	heart
28	chr3:119809000-119815000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:119809000-119816200	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr3:119809200-119809800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr3:119809200-119809800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr3:119809200-119809800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr3:119809200-119809800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:119809200-119809800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr3:119809200-119810000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr3:119809200-119810000	Flanking Active TSS	Hela-S3	cervix
37	chr3:119809200-119810000	Flanking Active TSS	NHDF-Ad	bronchial
38	chr3:119809200-119810200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:119809200-119810200	Flanking Active TSS	Brain Cingulate Gyrus	brain
40	chr3:119809200-119810200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
41	chr3:119809200-119810200	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr3:119809200-119810800	Active TSS	HepG2	liver
43	chr3:119809200-119811000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr3:119809200-119811200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:119809200-119811400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:119809200-119811400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr3:119809200-119812000	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr3:119809200-119812200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr3:119809200-119812600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr3:119809200-119814800	Active TSS	Brain Angular Gyrus	brain

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